Tracking Git commits

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Core commits

Recent Commits to bioperl-live:master

t/Tree/TreeIO/nexml.t: A close function was being used on
hmmer.t: Added tests to document "$hit->bits"
HMMERHSP: For HMMer report parsing, changed "$hsp->bits" to
Merge branch 'master' of
giving new meaning to the term "git", moving back where it belongs Another tweak to "_read_GenBank_Species" regex
memory adapter does not expect fasta database to be closed after initial load, so leave it open
adding back -DOH
fix parsing edge case
issue 12: changes to _translate_params that allow quoted option values
Merge branch 'master' of
Add to documentation, reorganize code a bit
spiced_seq() may need LWP
fix a warning in "_read_GenBank_Species", adjusted a regex to
Location/Split: Added its own "length" subroutine to
Fixing a change to a method name that works (_notes_file doesn't exist, _notes_path does)
Reverting the behavor of the index_dir method to silently do nothing if it doesn't find files to index, making it work with GFF files without fasta again.
(Thomas Sibley): Tell Storable to freeze and thaw CODE refs
Clean up and move to proper spot
Run commits

Recent Commits to bioperl-run:master

loosened validation for outfmt in BlastMethods to allow quoted multiple values (new blast+ feature); added tests for issue 12 to SABlastPlus.t
POD updates
Really die if EMBOSS is not found
I'm not sure if these programs will run on Windows now
Windows use 'NUL' instead of '/dev/null', so added the option
Added a way to find the required files in Windows using "dir"
Hmmer: Prevent errors caused by the presence of whitespace
Bowtie.t: "qx/ulimit -n 3>&-/" does not work as intended on Windows; In "reset_parameters", added an intermediary hash
BWA.t, Bowtie.t, Maq.t & Samtools.t: Moved tests using
AnalysisFactory_soap.t & Analysis_soap.t: Changed tests to 0.
Build.PL & MYMETA.json: Added SOAP::Lite v0.716 in
SoapEU-function.t: Updated expected version of a genome to current Some temporal files were not deleted
SABlastPlus.t: Added an additional $fac->cleanup for
SABlastPlus.t: Some bl2seq tests were giving hits even when the
Vista.t: The 'java Vista 2>&1' command to determine if Vista
FastTree.t & Neighbor.t: Fixed number of skipped tests and removed
BEDTools.t: Moved the file-finding lines inside the SKIP block,
Blat.t: Fixed skipped tests number and removed "$blat_present",
Ext commits

Recent Commits to bioperl-ext:master

moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet
use UPPPER_TOL to catch the case when the expectation maximization step
fixed Vitebi typo
Fixed the typemap and also a memory bug in viterbi function in HMM.xs
adding FEEDBACK:Support section to pod
Bump to 1.007 (similar to trunk)
ext patches (courtesy Thomas Jahns)
get rid of some unended comment warnings from C compiler
-fPIC needed for lib construction
include errno definition
removed DEBUG=1
IUPAC DNA support
IUPAC DNA test case
Add some helper code and tests to demo evalue oddities (bug 1857); casting issue?
Add cast to correct pointer type (get rid of warnings)
update version to last bioperl release
bug 2329
bug 2074/2329
Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this?
bug 2074
Bioperl-DB (BioSQL)

Recent Commits to bioperl-db:master

Minor POD edits and reformatting
Add some useful example code
updates since last release
update skipped files
buzgilla -> redmine
[RT 44466] remove corba-related scripts, now obsolete
squash perl 5.12 warning
ignore conf file
add minimal .gitignore file
weird duplication removed
committing patch for bug #2958
test commit to check SVN::Notify
Build.PL now checks for DBD drivers and attempts to DTRT
update Changes
fix empty POD section
some pod cleaning
main trunk version is wrong
* 02species.t now compared to similarly behaving instance, also creates comparable array
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